Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate WP_027720403.1 H589_RS0101635 branched-chain amino acid ABC transporter substrate-binding protein
Query= SwissProt::P21175 (373 letters) >NCBI__GCF_000425265.1:WP_027720403.1 Length = 377 Score = 212 bits (540), Expect = 1e-59 Identities = 123/341 (36%), Positives = 194/341 (56%), Gaps = 3/341 (0%) Query: 14 AMAIAGFASYSMAADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAGGVNGAQ-LE 72 A AI S + A T+K+ GP+TGP A G+ + G L A+E + + GG+ G +E Sbjct: 11 AAAILMLGSGMVFAKTLKLGTMGPLTGPYAADGNDIKNGVLTAVEVVKENGGIPGFDSIE 70 Query: 73 GVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITPSATAPE 132 + D AC+P+QAVA ANK++N+G VVG CSS+T PA+++ ++E ++MITP++T + Sbjct: 71 VLPQDTACEPRQAVATANKLINEGANGVVGAYCSSATLPASEVLDEESIIMITPASTNEK 130 Query: 133 ITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVKKTVEDA 192 +TSRG +FR G D+ QG +A KF+ E+ K++ ++ DK Y +G+A V+K + A Sbjct: 131 VTSRGLPYMFRMCGRDDDQGAIALKFMQEKLGAKSVYIVDDKTAYSQGLADGVEKMAKAA 190 Query: 193 GIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMG-LLLRQAKQAGLDARFMG 251 GIKV E +N GDKDF+A+++K+K Y + G L+L QAK+ G+ A + Sbjct: 191 GIKVLGHEHVNQGDKDFSAILTKVKTDNPDVFYMSMQNSATGALMLIQAKRMGIKAVRLA 250 Query: 252 PEGVGNSEITAIAGDASEGMLATLPRAFEQDPKNKALIDAFKAKNQDPSGIFVLPAYSAV 311 + V + ++ IA DA+E + T + P K ++ K +P G + AY + Sbjct: 251 QDAVYHPQLIEIAKDAAEDVYLTFGFIDDNAPAYKEFYAKYQPKYGNP-GAYSGYAYDSA 309 Query: 312 TVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGD 352 K ++ AG DPEKV L ++ T ++ F GD Sbjct: 310 IAYLKAVKAAGSTDPEKVKAELMKLDYDGATKHIKFKANGD 350 Lambda K H 0.316 0.133 0.377 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 316 Number of extensions: 18 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 373 Length of database: 377 Length adjustment: 30 Effective length of query: 343 Effective length of database: 347 Effective search space: 119021 Effective search space used: 119021 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory